Evaluation of Prebiotics through an In Vitro Gastrointestinal Digestion and Fecal Fermentation Experiment: Further Idea on the Implementation of Machine Learning Technique.

Prebiotics are non-digestible food ingredients that promote the growth of beneficial gut microorganisms and foster their activities. The performance of prebiotics has often been tested in mouse models in which the gut ecology differs from that of humans. In this study, we instead performed an in vitro gastrointestinal digestion and fecal fermentation experiment to evaluate the efficiency of eight different prebiotics. Feces obtained from 11 different individuals were used to ferment digested prebiotics. The total DNA from each sample was extracted and sequenced through Illumina MiSeq for microbial community analysis. The amount of short-chain fatty acids was assessed through gas chromatography. We found links between community shifts and the increased amount of short-chain fatty acids after prebiotics treatment. The results from differential abundance analysis showed increases in beneficial gut microorganisms, such as Bifidobacterium, Faeclibacterium, and Agathobacter, after prebiotics treatment. We were also able to construct well-performing machine-learning models that could predict the amount of short-chain fatty acids based on the gut microbial community structure. Finally, we provide an idea for further implementation of machine-learning techniques to find customized prebiotics.

Rahnella laticis sp. nov. and Rahnella contaminans sp. nov., and emended description of the genus Rahnella.

Taxonomic positions of six isolates, which were recovered from two different environments in Jeju, Republic of Korea, were examined by a polyphasic analysis. Cells of the isolates were Gram-reaction-negative, facultatively anaerobic, motile and rod-shaped and showed growth at 4-30 °C, pH 4.0-9.0 and with 0-6 (w/v) NaCl. In phylogenomic analysis based on 92 single-copy core genes, it was shown that the isolates belonged to the genus Rahnella and formed three distinct sublines within the genus. The isolates shared 16S rRNA gene sequence similarities of 97.9-100 % with one another. The isolates contained ubiquinone-8 was as the major isoprenoid quinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The predominant fatty acids were C16 : 0 and C17 : 0 cyclo. The G+C content of their genomic DNA was 52.8-53.1 %. Average nucleotide identity and digital DNA-DNA hybridization values supported that strains SAP-17T and Lac-M11T represented two new species of the genus Rahnella, whereas strain SAP-10 was a strain of Rahnella victoriana. Based on the results obtained here, Rahnella laticis sp. nov. (type strain SAP-17T=KCTC 72960T=NBRC 114723T=CCM 9079T) and Rahnella contaminans sp. nov. (type strain Lac-M11T=KACC 21743T=NBRC 114406T) are proposed. Also, an emended description of the genus Rahnella is given on the basis of our physiological and chemotaxonomic results.

Duganella aceris sp. nov., isolated from tree sap and proposal to transfer of Rugamonas aquatica and Rugamonas rivuli to the genus Duganella as Duganella aquatica comb. nov., with the emended description of the genus Rugamonas.

A Gram-reaction-negative, strictly aerobic, betaproteobacterial strain, designated SAP-35T, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea, and its taxonomic status was examined by a polyphasic approach. Cells of the organism were non-sporulating, motile rods and grew at 4-30 °C, pH 6-7 and in the absence of NaCl. 16S rRNA gene- and whole genome-based phylogenetic analyses showed that strain SAP-35T belonged to the family Oxalobacteraceae and was closely related to Rugamonas rivuli (98.9% 16S rRNA gene sequence similarity) and Rugamonas aquatica (98.4%). The phylogenomic clustering and average amino acid identity values supported that strain SAP-35T belonged to the genus Duganella and two Rugamonas species should be transferred to the genus Duganella. The major isoprenoid quinone of the isolate was Q-8. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The predominant fatty acids were summed feature 3, C16:0 and C17:0 cyclo. The G + C content of genome was 64.9%. The average nucleotide identity and dDDH values between strain SAP-35T and the members of the genera Rugamonas and Duganella were < 85.1% and < 49%, respectively. Based on the combined data presented here, strain SAP-35T (= KCTC 72227T = NBRC 113903T) represents a novel species of the genus Duganella, for which the name Duganella aceris sp. nov. is proposed. Also, Rugamonas aquatica Lu et al. (Int J Syst Evol Microbiol 70: 3328-3334, 2020) and Rugamonas aquatica Lu et al. 2020 are reclassified as Duganella aquatica comb. nov., with the emended description of the genus Rugamonas.

Rahnella aceris sp. nov., isolated from sap drawn from Acer pictum.

A Gram-reaction-negative, facultatively anaerobic bacterium, designated SAP-19T, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea and its taxonomic statue was investigated by a polyphasic approach including genome- and 16S rRNA gene-based phylogenetic analyses. Cells were motile, short rods and showed growth at 20-30 °C, pH 4-9 and 0-6% (w/v) NaCl. The whole genome- and 16S rRNA gene-based phylogenetic analyses exhibited that strain SAP-19T belongs to the genus Rahnella and forms a tight cluster with Rahnella aquatilis. The isolate shared average nucleotide identity of 92.7% and 16S rRNA gene sequence similarity of 99.6% with the type strain of Rahnella aquatilis. The polar lipids contained phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified lipid. The major isoprenoid quinone was Q-8. The predominant fatty acids were C16:0 and C17:0cyclo. The G + C content of the genome was 52.3%. The low average nucleotide identity (92.7%) and digital DNA relatedness (48.6%) values between the isolate and the most closely related strain showed that the isolate can be considered a different genospecies. On the basis of combined data obtained in this study, strain SAP-19T (= KACC 21744T = NBRC 114407T) represents a novel species of the genus Rahnella, for which the name Rahnella aceris sp. nov. is proposed.

Spiraea prunifolia var. simpliciflora Attenuates Oxidative Stress and Inflammatory Responses in a Murine Model of Lipopolysaccharide-Induced Acute Lung Injury and TNF-α-Stimulated NCI-H292 Cells.

Spiraea prunifolia var. simpliciflora (SP) is traditionally used as an herbal remedy to treat fever, malaria, and emesis. This study aimed to evaluate the anti-oxidative and anti-inflammatory properties of the methanol extract of SP leaves in tumor necrosis factor (TNF)-α-stimulated NCI-H292 cells and in a lipopolysaccharide (LPS)-induced acute lung injury (ALI) mouse model. SP decreased the number of inflammatory cells and the levels of TNF-α, interleukin (IL)-1ß, and IL-6 in the bronchoalveolar lavage fluid, and inflammatory cell infiltration in the lung tissues of SP-treated mice. In addition, SP significantly suppressed the mRNA and protein levels of TNF-α, IL-1ß, and IL-6 in TNF-α-stimulated NCI-H292 cells. SP significantly suppressed the phosphorylation of the mitogen-activated protein kinases (MAPKs) and p65-nuclear factor-kappa B (NF-κB) in LPS-induced ALI mice and TNF-α-stimulated NCI-H292 cells. SP treatment enhanced the nuclear translocation of nuclear factor erythroid 2-related factor (Nrf2) with upregulated antioxidant enzymes and suppressed reactive oxygen species (ROS)-mediated oxidative stress in the lung tissues of LPS-induced ALI model and TNF-α-stimulated NCI-H292 cells. Collectively, SP effectively inhibited airway inflammation and ROS-mediated oxidative stress, which was closely related to its ability to induce activation of Nrf2 and inhibit the phosphorylation of MAPKs and NF-κB. These findings suggest that SP has therapeutic potential for the treatment of ALI.

Marimonas lutisalis sp. nov., isolated from a tidal mudflat and emended description of the genus Marimonas.

A Gram-reaction-negative bacterial strain, designated GH1-19T, was isolated from a tidal mudflat sample collected in Gangwha Island, Republic of Korea. Cells of the novel micro-organism were strictly aerobic, non-sporulating, motile and rod-shaped. Growth occurred at 10-40 °C (optimum, 30 °C), pH 6-9 (pH 8) and in the presence of 1-9 % NaCl (3 %). Comparative analysis of complete or nearly complete 16S rRNA gene sequences exhibited that strain GH1-19T formed a distinct cluster between Marimonas arenosa CAU 1311T (97.42 % sequence similarity) and Aquicoccus porphyridii L1 8-17T (97.35 %). Similarity levels of 16S rRNA gene sequences between the novel strain and other members of the family Rhodobacteraceae were below 96.6 %. The isoprenoid quinone was Q-10. The major fatty acids were C18 : 1ω7c, C16 : 0, summed feature 3 (C16 : 0 ω7c and/or C16 : 0 ω6c) and C12 : 0 3-OH. The polar lipids consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. The G+C content of the DNA was 63.2 mol% (draft genome). DNA-DNA relatedness value between the novel strain and the type strain of Marimonas arenosa was 12.7±9.0 %. On the basis of data from phenotypic, chemotaxonomic and DNA-DNA hybridization studies together with phylogenetic analyses, strain GH1-19T (=KCTC 62376T=DSM 106292T) represents a novel species of the genus Marimonas, for which the name Marimonas lutisalis sp. nov. is proposed, with the emended description of the genus Marimonas.

Nonvolatile memory thin-film transistors using biodegradable chicken albumen gate insulator and oxide semiconductor channel on eco-friendly paper substrate.

Nonvolatile memory thin-film transistors (TFTs) fabricated on paper substrates were proposed as one of the eco-friendly electronic devices. The gate stack was composed of chicken albumen gate insulator and In-Ga-Zn-O semiconducting channel layers. All the fabrication processes were performed below 120 °C. To improve the process compatibility of the synthethic paper substrate, an Al2O3 thin film was introduced as adhesion and barrier layers by atomic layer deposition. The dielectric properties of biomaterial albumen gate insulator were also enhanced by the preparation of Al2O3 capping layer. The nonvolatile bistabilities were realized by the switching phenomena of residual polarization within the albumen thin film. The fabricated device exhibited a counterclockwise hysteresis with a memory window of 11.8 V, high on/off ratio of approximately 1.1 × 10(6), and high saturation mobility (µsat) of 11.5 cm(2)/(V s). Furthermore, these device characteristics were not markedly degraded even after the delamination and under the bending situration. When the curvature radius was set as 5.3 cm, the ION/IOFF ratio and µsat were obtained to be 5.9 × 10(6) and 7.9 cm(2)/(V s), respectively.